Nayacalevu, who also started in the World Cup opener against England, injured his right knee five minutes into the Wallabies Test.
He will now return to his French club Top 14 champions Stade Francais for rehabilitation.
Nagusa, who was considered unlucky not to make the initial World Cup squad, will join the side ahead of their next game against Wales in Cardiff on Thursday.
Fiji came into the tournament with high hopes of causing an upset in the tough Pool A but have lost both their first two games. – Agence France-Presse